#
# Licensed to Big Data Genomics (BDG) under one
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# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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#
library(bdgenomics.adam)

context("manipulating variants")

ac <- createADAMContext()

test_that("round trip vcf", {
    testFile <- resourceFile("small.vcf")
    variants <- loadVariants(ac, testFile)
    tmpPath <- tempfile(fileext = ".vcf")
    saveAsVcf(toVariantContexts(variants), tmpPath)

    expect_equal(count(toDF(variants)), count(toDF(loadVariants(ac, tmpPath))))
})
